The Ancient Conspiracy is nearly ready to make their big move and conquer the world. Their mad scientists have perfected a new and incomprehensibly powerful form of Applied Phlebotinum that will overpower any conventional armies that stand in their way.

There's just one... small... problem...

Either

The Mad Scientists tested it out on an unwilling victim who has now escaped,

The victim was willing, but the process was flawed and produced an uncontrollable Psycho Prototype.

The phlebotinum has somehow been removed from the labs and fallen into the hands of someone who knew diddly about the Conspiracy but isn't inclined to go along with them.

The phlebotinum itself, if it has intelligence of some sort, has flat-out gone rogue. Sometimes the bad guys take a good guy, upgrade him, and are interrupted before they can do any brainwashing.

Even if the beneficiary of the phlebotinum is not initially opposed to the Conspiracy, it won't be long before they Kick the Dog or otherwise cross the Moral Event Horizon in their efforts to get their technology back. We now have ourselves a Phlebotinum Rebel: empowered by the bad guys to be the only person capable of defeating them. Bravo, Evil Overlords.

In Bleach you find out that Aizen orchestrated EVERY SINGLE EVENT that led to Ichigo becoming so unbelievably powerful. Just to absorb him. In the end, however, things backfired and Ichigo and Urahara defeat Aizen.

Ikuro Hashizawa from Baoh The Visitor (implanted with a brain parasite that transforms him into an armored, acid-touched, needle-hair-throwing killing machine... but which will kill him in 111 days as it reproduces).

Sho Fukamachi from Guyver stumbles across one of the only three Bio-Booster Units left on Earth, after they are stolen from Kronos.

Guyver III is an even stronger case, as he bonded with a G-Unit specifically to take Kronos down. Of course, he wants to take over the world himself and sees Sho as more of a tool than a friend or ally.

There is yet another example in the form of Masaki Murakami, who was one of a number of humans used as "practice" to upgrade one of the villains' powers, but managed to escape. Somewhat subverted, as he's since become the new 13th Zoalord, Imakarum.

Then there's former Zoalord Richard Guyot, who looks to have survived having his zoacrystal ripped out by Archanfel. And Aptom, an irreproducible "Lost Number" who just decided to stop obeying orders one day. And the recent female Guyver, seen tearing up a Kronos compound for reasons unknown... Come to think of it, is there a single enemy of Kronos that isn't powered by their own Phlebotinum?

Hagane Yakushimaru from Hagane, a semisequel to Xenon: the Red Sea has branched out into genetics and uses "parasite DNA" culled from highly skilled dead people to grant their skills to the living. This will eventually cause the recipient's mind to be completely overridden by the donor's. Hagane, a high school girl (for a change), has been given the sword skills of Miyamoto Musashi; she joins up with rebels who've been dosed with Billy the Kid and Hanzo Hattori.

The kids from Project ARMS, given super-powered nanotech prosthetic limbs by the immensely influential Egrigori conspiracy.

Partly subverted in Parasyte, in that we never actually run into whoever dispatched the Parasites to Earth.

Dr. Jail Scaglietti of Magical Girl Lyrical Nanoha is a Mad Scientist obsessed in creating Artificial Mages. His work comes to fruition when Precia Testarossa, grieving over the loss of her daughter, completes his research through Project Fate and creates the first successful Artificial Mage through cloning. As the creation of Artificial Mages are explicitly banned by the Time-Space Administration Bureau, Jail is considered an inter-dimensional criminal, and by the third Season, has had a highly-ranked enforcer tracking his every move for many years. The name of the enforcer? Fate Testarossa Harlaown. Let's just say that her name isn't a coincidence.

Subaru and Erio, who are products of the same research, participated in thwarting his plans too.

Tongpu in the Cowboy Bebop episode "Pierrot le Fou" underwent secret biological enhancements aimed at turning him into a super-soldier, but the process drove him insane. He made a bloody escape from a secure facility and became an almost-unstoppable assassin—the Mad Clown of the title—with the mind of a demented child.

Daisy-023, Ralph-303, Joseph-122, and two other Spartan trainees in the Homecoming segment of Halo Legends, who escape the training facility on Reach to go back to their own homes. Joseph gets caught before even getting off the planet, the two guys commit suicide after finding out that they've been replaced with clones (and killing said clones), Ralph and Daisy both rejoin the program, and get killed fighting the Covenant.

Chrona in the Soul Eater manga does it TWICE, once against Medusa and the other time back to her again.

Ichise in Texhnolyze is this initially. He was given cybernetics, usually reserved for the upper class, by a Doctor with a willful and independent streak herself, so she either expected it or was willing to accept it as a consequence of experimenting with the hardware's limitations. Eventually he comes back around to supporting Onishi, but that's after he's fallen from favor with the ruling circle and become a rebel himself.

Maggie, Michelle and Anita of R.O.D the TV are an example of this. It was a revealed that Paper Users were fabricated and there'd been multiple teams of "Paper Sisters", but were all conveniently killed before the start of the series. However, though they were never related to begin with, Anita takes this time to get mad at them for not actually being her sisters. However, she gets over herself and they later bring all of Dokusensha to its knees.

The three cybernetically modified animals from WE 3 were created by the government and escaped with the help of their veterinarian. They didn't really know what to do when they left.

In Fleetway's Sonic the Comic, Dr. Robotnik once copied his own brain patterns and put them in a super powerful robot body so he would have a competent underling, failing to consider whether or not a physically superior version of himself would be too happy with that arrangement.

Spawn: The dead guy turned into a Noble Demon by Hell, who wanted him as an assassin. Didn't turn out so well for them.

Dagon of Team Titans is a really idiotic example of this. So you're an evil mad scientist in the pay of a tyrannical dictator, and you've decided it would be neat to give him some vampire soldiers by infusing normal humans with Dracula's DNA. Naturally, the person you test the process out on is a captured member of the rebel forces who really, really hates everyone on your side... yeah. This works out about like you'd expect.

Universe X turned Captain America (comics) into an example of this via its standard Retcon technique, revealing that the Super Soldier Serum was actually a Nazi research project carried out by German moles working in the US. Makes a twisted kind of sense in some ways (take a look under the mask, after all), but seems unnecessarily risky.

X-O Manowar of Valiant Comics was a tenth-century Visigoth kidnapped by evil aliens. He promptly broke free, bonded with the most powerful Powered Armor suit they could build, and escaped to (thanks to relativistic time dilation) 1990s Earth.

Wolverine of X-Men was already a highly skilled, experienced, and ferocious soldier when he received an indestructible skeleton from Weapon X. However, he was not happy when he woke up in a water tank with no idea who he was, where he was, or what the hell he was doing there...

Friday in Rogue Trooper turned against Highsight when he discovered they were commanding both sides.

The Authority: Apollo and Midnighter. Originally, they were created as part of a secret superhero team by Stormwatch Weatherman Henry Bendix. Unfortunately, Bendix was a total psychopath, and sent his loyal creations into a trap to be destroyed. Apollo and Midnighter were the only ones to escape with their lives, and it took many years (and the death of Bendix) for them to reconcile with Stormwatch.

In Flashpoint's Project: Superman, a miniseries which stars an alternate version of Apollo, he is once again a super soldier, but becomes a Psycho Prototype after being pumped full of Doomsday's DNA and treated like a monster by those who created him. After killing some of his own squad on a mission, he's locked away for years, and then orchestrating an elaborate escape plan.

Ghost Rider: Ghost Rider was bound to a demonic power, which he then uses to fight evil.

Subverted in Captain Atom: Nathaniel Adam was certainly not a completely willing test subject of the Silver Shield Project (he had been falsely convicted of murder and treason, and volunteering was the only way to avoid his sentence), and he had every reason to hate the head of the project, Wade Eiling, and neither Eiling, Megala, nor anyone else on the project had any idea that it would give Nate incredible superpowers, but despite all of that, Eiling was still able to manipulate Cap into working for him.

In Terminator: Salvation the character Marcus is turned into a Cyborg and persuaded (his memories are erased and new ones are implanted) to help John Connor and lead him to the Skynet base. Once he finds out he was actually doing Skynets bidding, as intended, he tears away his link to Skynet to help the rebel cause. In the end he gives his own life (well, his still-human heart) to save John who was mortally wounded.

Of course, if Skynet hadn't bothered to send a Terminator back in time in the first place, Sarah Connor would have been just another waitress and John Connor would never even have been born.

And Skynet never would have been created in the first place.

The Alternate Ending has John Connor DIE, and Marcus assume the identity.

In Meatball Machine, the main character gets partly infested with one of the alien parasites. All it does is make him a BadassHollywood Cyborg, unlike the other characters that it happens to.

RoboCop: The first and third movies featured the heroic version, and the sequel featured the villainous version.

In The Incredible Hulk (2008), we have the borderline sociopathiccharming and dedicated Emil Blonsky, who was already hopped up on a supersoldier cocktail before receiving a further injection of Hulk serum on top of that. The only justifaction given for pimping out a mental case like that was to catch Bruce Banner, who is an okay guy if you don't piss him off.

Well, that and Mr. Blue just wanted to see what would happen.

Blue:(while being choked, and after warning about side effects) I... didn't say... I was unwilling."

Of course, it wasn't the Hulk serum that made him mentally unstable, it was the incomplete supersoldier serum. Blonsky was a pretty cool guy prior to that injection. Just a guy doing a job with no interest in ever being more than a soldier. A man seeking a Worthy Opponent in the form of a challenging mission. A man who does what he does, and wants to do it well. Like the general himself, Blonsky becomes a bit obsessed with the power of the Hulk. The deleted scenes go on to enforce this interpretation of the character, and stress the imperfections of the supersoldier serum.

Kiryu (a.k.a. Mechagodzilla 3) is a cyborg created from the remains of the original 1954 Godzilla. Because of this, he ends up destroying a good portion of Tokyo when he heard Godzilla's roar causing him to override the commands given to him by the JSDF and start rampaging like his flesh-and-blood counterpart.

Likewise, the film Godzilla VS Spacegodzilla has the heroes try to control Godzilla via Mind Control telepathy. It doesn't work...

Two words: Jason Bourne. Plus another four, for emphasis: in the movies only.

To elaborate:

Movies: Bourne is an amnesiac former CIA agent from an illegal assassination program who finds he doesn't like the person he was and turns against his corrupt superiors.

Books: his superiors were sort of white hats, the Big Bad is the super-assassin he went after before his amnesia, and the Bourne-vs-CIA subplot is a big misunderstanding/enemy plot.

And that's only the tip of the ice berg for how different the book and movie are.

Wikus van der Merwe from District 9. After exposure to a mysterious alien fluid, Wikus is subjected to horrifyingly painful, and disturbingly cruel experiments that reveal that he's the only human capable of using the technology of the alien refugees. Once he escaped, being forced into a corner as a wanted man resulted in his eventually being forced to turn things around on MNU in an attempt to acquire a cure and gain his life back.

Resident Evil: Firstly Alice falls under this trope. Biogenetically engineered into a supersoldier who then procedes to turn against Umbrella

Also Nemesis follows the same path in Resident Evil Apocalypse after almost being killed by Alice. He rediscovers his former humanity and also fights back against Umbrella

The power-boosting serum in Push gave Kira much greater than normal abilities. Its administration was immediately followed by her breaking out of Division and working to bring them down.

To an extent, Boba Fett from Star Wars. The first clone trooper, left Kamino with his dad, came back as in adult to lead an Imperial attack.

A better example would be Spar, a clone trooper who broke ranks and joined the Confederacy.

IG-88, straight up.

In Megamind, the title character gives the power of his now-deceased archnemesis, Metro Man, to a random schlub, Hal Stewart, creating the superpowered Titan. In an interesting take on the trope, Megamind actually *wants* his Phlebotinized creation to fight against him; but it rebels nonetheless by playing a little too rough.

In Captain America, Steve Rogers was the second augmentee: it increased his good personality, so he became Captain America. Johann Schmidt was the first: the procedure increased his evil personality, so he became Red Skull. The appearance part might just have been an imperfection of the procedure. Schmidt has Dr. Erskine killed because Schmidt doesn't want Erskine to replicate his "success"..

In Dan Simmons' Illium and Olympos, a scholar is granted powers by the Goddess Athena to view and record The Trojan War. But it's all Applied Phlebotinum -- the Gods and Goddesses of Olympos are actually evolved humans using Magic From Technology. The scholar rebels.

Dean Koontz' Frankenstein trilogy, in which a version of the classical monster is fighting his titular creator's plan to replace humanity with with his soulless creations.

This was basically Karl Marx's view of the bourgeoisie, as expressed in his speculative fiction classic The Communist Manifesto.

In Kurt Vonnegut's Report on the Barnhouse Effect, Professor Barnhouse discovers how to use his mind to destroy objects. The US military is quite interested and sets up some tests for him to destroy missiles and tanks. Barnhouse decides that he is the first weapon with a conscience, and subsequently goes into hiding. He then decides to destroy all the military weapons in the world.

Piggy of Wraith Squadron in the X Wing Series. A Gammorean modified in a laboratory to be less emotional and better at logical thinking, he escaped and joined the New Republic. All the other test subjects committed suicide were killed when their creator gathered them together and committed suicide by mixing volatile chemicals and blowing the entire room up.

The pilots also make Wedge pretend to be a modified Ewok in the same novels when they disguise themselves as Space Pirates.

In Mad Skills by Walter Greatshell, Madeleine Grant is essentially a Super Prototype for a system that uses leech brain cells to increase the human brain's potential to Singularity levels, who can be commanded to kill at a distance by her doctors. Turns out, she's really good at slipping the leash, and she's not happy about having her chain jerked by a bunch of Mad Scientists.

Mordion Agenos, the Reigners' Servant from Hexwood. Servants are the product of careful selective breeding for Reigner traits (Mordion can stop people's hearts using his mind alone) and a Training from Hell that generally results in a kind of Stockholm Syndrome - but Mordion comes out of the other end with a conscience intact, and when the Bannus allows him to forget about the hold of fear the Reigners have over him, it's very bad news for the Reigners.

In Catherine Asaro's books about the Skolian Imperialate, the Aristos take genetic samples from bodies of former rulers of the long-dead Ruby Empire, in order to create a brother and sister pair meant for breeding into pleasure slaves. Pleasure, in this case, means physically torturing the slave so that the pain the slave telepathically radiates causes an orgasmic response in the telepathically receptive Aristo. The brother, name unknown, kills himself upon realizing his intended purpose. The sister is Layahalia Selei, who kills her captors, escapes, discovers a Lock into an abandoned FTL communication system, and eventually founds the Imperialate. The Imperialate is now the only society capable of holding the Aristos at bay from conquering the entire galaxy.

In Colin Kapp's The Ion War, the process of "para-ion transformation" makes soldiers temporarily immune to just about all weapons fire. But the transformation is so very painful—every time—that only convicts sentenced to death can be recruited. Naturally, this means they've got little or no reason to be loyal ... and the project has already been infiltrated by rebel agents, trying to persuade the "ion warriors" to defect....

The plot of most of the Showa (1970s-1980s) Kamen Rider series, along with Kikaider and a few other Toku productions, begins with the hero-to-be getting kidnapped and upgraded against his will. You really have to wonder why bad guys don't brainwash victims and then make them all-powerful. Their creator, Shotaro Ishinomori (who also did Cyborg 009), may as well be the patron saint of this trope.

Shows up in the modern era most prominently in the American toku show, Power Rangers RPM, where the Black Ranger, Dillon, had escaped from the Machines' experiments after they filled him with body-enhancing hardware, but before they got to his brain.

Heisei Kamen Rider series use another variety: It's usually the conspiracy that created the Rider gear, and it fell into the hands of someone who'd rather kick their butts than give it back or serve them. This time, the conspiracy is usually an entire species themselves (see the Orphenochs and in a senseFangires). Kamen Rider Double does it both ways, with the Rider tech falling into Shotaro's hands, and Philip beingPhlebotinum and escaping.

Dark Angel would have no plot at all without this. Twelve X5 Super Soldiers (Max, Ben, Zack, etc.) escaped from Manticore as children and went on the run, though Manticore retained several (including clones of the escapees, and monsters of the week) until the organization was brought down 11 years later and everyone escaped.

A reverse example in Stargate Atlantis is the character Michael who uses the experiments done on himself and his kind to empower himself as a supervillain.

The Replicators are also involved in similar experiments. Once, they made nanite-built flesh-and-blood copies of the team who, upon discovering their true identities, rebelled against them. However, it turned out that the Replicator faction creating them were themselves rebels who wanted to figure out a way to Ascend. Later, the remnants of said faction managed to perform a perversion of Ascension by uploading their minds into subspace but they quickly changed their minds and invaded Atlantis' systems, rebuilding their bodies. Weir experimented with building flesh-and-blood bodies again to Ascend (this time for real) but one member rebelled and caused some trouble.

Star TrekTNG: Roga Danar and the other exiled Angosian soldiers, in "The Hunted", with a Vietnam Veteran Syndrome metaphor Anviliciously applied.

The episode is basically First Blood, the first Rambo movie, with Phlebotinum added.

Composite!Echo is the standard version done quite literally. Alpha sought to create another composite like himself. It worked. The composite decided to attack him.

In Doctor Who this was what the Master became. Enraged on learning he had been manipulated and modified his entire life to act as a tool for his people's final, desperate plan, in The End of Time, he lashed out against their leader and brought the plan crashing down around them.

Also, Melody Pond/River Song, raised as a weapon to kill the Doctor, but runs off and falls in love with him instead.

Averted and Lampshaded in the GURPS Infinite Worlds setting. The Nazis of Reich-5 have developed various means of giving people the psychic or mystical ability to travel between alternate worlds. Despite the horrific effects these methods have on the users, only loyal SS members are selected for the treatment, rather than the usual victims; the idea of accidentally creating world-jumping Jews, Gypsies, or Slavs is obviously way too risky!

This is a large part of the Summer Court's game in Changeling: The Lost. The Autumn Court, though less... militant about the whole affair, are arguably a purer example, dedicated to using Fae magic against the Gentry. (Summer Courtiers are not adverse to doing the same, but hey, a good, sturdy cold iron crowbar or shotgun is just as good as Changeling powers if it gets the job done!)

Forgotten Realms has it exploited with "Chosen Ones" - monstrosities Red Wizards sometimes create from slaves. The process leaves Chosen One tortured into blindly lashing out madness, and mind control involved makes one see targets as the wizard who did it to him, and thus fight in constant frenzy. It's not very widespread, because sometimes the control slips, at which point "Chosen One" screams, turns and runs off to find its real creator, ignoring anything that doesn't stand on the way.

Spelljammer has Bionoids, shapeshifters created by elves as living weapons in the First Unhuman War. Later elves took a habit of treating them like some sort of inferior beasts, so once the Second Unhuman War started, many bionoids chose to participate - this time, on the other side. Or, as in The Radiant Dragon -

Vallus: That's impossible. [...] why would they serve orcs? They are elven weapons.Teldin': You probably can't understand this, Vallus, but you just answered your own question. (walks out on him)Vallus: ...

This troper wrote a 3.5 edition D&D campaign based on the fact that half-dragons don't make sense: a pair of explorers got trapped in an ancient buried city and came across a half-dragon (a magical experiment) who had been in stasis for several thousand years.

The Green Sun Princes are often noted to be really likely to end up turning on their masters and creators, or at least abandon their intended purpose and start forging their own path.

The Abyssals can try, but the Neverborn were smart enough to incorporate countermeasures; Abyssal powers are only really good for killing things (meaning that whatever they're used for, they'll be advancing the cause of the Neverborn) and trying to do anything other than killing just doesnotwork.

Until they're redeemed, and thereby become the purest representation of what a Solar Exalt is capable of since the Primordial War... given that the Neverborn freed them from the Great Curse (which instills madness in those subject to it). Good job fixing it, villains.

It should also be noted in-setting that this is what led to there being Yozis and Neverborn in the first place. They were once the Primordials, who put the gods, their servants, in charge of running Creation while they faffed about with the Games of Divinity, and gave them both phenomenal godlike power and the geas never to harm their masters. Funny thing about that—there was no geas saying that gods couldn't empower humanity to harm their masters...

The entire plot of Pokémon Colosseum is a case of this. You play a hero, or perhaps as he is a thief, an Anti-Hero, who has run off with the only portable Snag Machine of Team Snagem, and are the only one who can stop Team Snagem as well as their shadowy beneficiaries, Cipher by use of this machine. It is indicated the Hero initially has no grudge, he's presumably just not into the gang mentality anymore, until he saves The Chick, who is important to revealing Shadow Pokémon and sets him on his journey.

To be fair, Wes announces his resignation in the form of blowing the bloody hell out of Team Snagem HQ. There was probably a little pre-existing bad blood there. Or Wes is just batshit insane.

Similarly, Final Fantasy IX has world-stealing badnik Garland brought down by his own creations, Kuja and Zidane, created to be his "angels of death".

Garland: Regrettable... I thought your soul would be perfect for a new angel of death...Zidane: I AM the new angel of death! Yours!!!

Terra from Final Fantasy VI. You actually start the game controlling her and the Empire's soldiers. Especially stupid in that there really isn't any reason for her to have rebelled; Kefka just really wanted to try out a Slave Crown that resulted in memory loss when it was destroyed. Nice one, Kefka.

Likewise, General Celes betrays the Empire after realizing how corrupt and evil it is, and she'd been made into a MagitekSuper Soldier by them. Though technically she was born as one. After the debacle of Kefka, the Empire decided that Magitek infusion of adults was a bad idea...so they genetically engineered a "perfect soldier" and gave her the infusions while she was still in the womb.

In fact, Kefka himself falls under this trope. Kefka wasn't insane until he underwent some Magitek experiments instigated by the Empire. Apparently, he was a perfectly normal, well-adjusted guy. Not just well-adjusted; the best General in the entire Empire, and he'd recently ascended to Prime Minister, second only to Gestahl himself. Then he became an Omnicidal ManiacEvil Clown who eventually ends up killing Emperor Gestahl himself, and wiping out The Empire to all but the last man.

The fact that the Emperor personally killed her mother. Might have been a reason for Terra to rebel should she find out, the Slave Crown was still a pretty dumb idea though.

Final Fantasy VIII does this twice. The first time, the SeeDs created by Garden are betrayed by the creature that's set everything up, the Garden Master NORG. The SeeDs' response is distinctly lethal. The second case involves the Big Bad Ultimecia's Evil Plan involving turning Rinoa into a Sorceress at the end of the second disc. Though she doesn't have much control over her capabilities, the Angel Wing Limit she gains as a result is ludicrously powerful and is quite effective if you know how to use it.

Chrono Cross: Serge was accidentally made the "Arbiter" of FATE as a child, but ends up defeating FATE himself when the convoluted plot leads him there.

Valkyrie Profile: Odin creates Lenneth the valkyrie out of a human girl and sends her to prepare the world for Ragnarok, but (at least in two out of three endings) she rebels against his grip on the world and overthrows him. Something similar happens in the sequel, too.

In Quake IV, the player gets Stroggified—or, nearly so. He's strapped to the Conveyor Belt O' Doom, which proceeds to cut off and replace various appendages and inject him with things, including something that acts as Translator Microbes for the Strogg language, but his squad breaks in and gets him out before the brainwashing could start. He promptly saves said squad from another freshly-Stroggified human who wasn't so lucky. Watch the whole thing here! Kane then gets the benefits of understanding the Strogg language and having superior running and leaping abilities, and the detriment of being loathed by most humans. Though he never protests the latter.

In Portal, GLaDOS possibly regrets giving the player character the portal gun when she uses it to escape from the furnace she was being dumped into, then find her way into GLaDOS' room and destroy the computer. Maybe.

As does BioShock (series) 2. You may know that you control a Big Daddy in that one; not just any Big Daddy, but the prototype.

Far Cry: Instincts plays this straight, with the feral-power boosted Jack Carver proving to be the greatest success of Doctor Krieger's project. If only they hadn't destroyed his boat to get him in the first place....

Metal Gear Solid. Oh dear, Metal Gear Solid. At least five of the characters perfectly fit this mold: Solid, Liquid, Solidus, Gray Fox and Raiden. Although with the Mind Screw-y-ness intrinsic to the series, it's really hard to say whether half of those actually are rebelling.

Literally every time FOXHOUND has appeared (Metal Gear, Metal Gear 2, Metal Gear Solid, and Ghost Babel), one or more members have gone rogue. It's enough to make you wonder why the government keeps on recruiting.

The protagonist of the Crusader games is an unusual example in that though he rebels, he's not the only one of his kind. Indeed, he and his fellow Silencers may well be mass-produced.

Jak from Jak II. The Evil Overlord pumps him full of Dark Eco in an attempt to create a "Dark Warrior," but Daxter manages to spring Jak from his prison. Double Whammy in that it turned Jak from a starry-eyed kid with some elemental powers into a Determinator Badass with a Super-Powered Evil Side.

By that same token, Clank's "mother" (the computer controlling robot production) counts as well.

Deus Ex. While J.C. Denton may not be entirely unique, given that both his 'brother' and The Dragon are nanotech-augmented agents as well, he otherwise practically embodies the trope.

Notably, there's very little Wangst here. No-one in Deus Ex rebels because of what they are or were made into, but more often from political differences or one too many Kick the Dog moments by the bad guys.

Both Denton brothers are examples; Paul rebels first and makes it somewhat necessary for J.C. to follow suit.

The animations, lip sync, environment, and voice acting files to avert this trope are on the install disk; the development team simply didn't link them into the final game, as there were already so many options they had to account for in the quests. If you link the files together you are treated to a scene where dialogue options allow you to have JC turn down Paul's request that he join the NSF, saying: "I may not agree with everything they do, but I'm not a terrorist". It's just too bad this option didn't make it into the final game.

Shows up in a small way in The Suffering. The only reason the protaganist survives the initial attack by the physics-defying, wall-crawling monters is by taking out a blade -left- in the bodies of one of the first victims. Way to go, evil death-zombies.

Geist has John Raimi's spirit separated from his body and put into a brainwashing/ghost training machine, but the machine gets sabotaged and he escapes to wreak havoc on the facility and release a lot of Demonic Invaders while trying to keep the same thing from happening to a friend. He's far from the only spectral operative around, and gets recaptured and put back in the machine. This doesn't work either, because the demons are running amok and break it again. Raimi then goes on to foil all the bad guys before their plans are fully in motion.

City of Heroes/Villains has a few examples, most obviously the hero Synapse.

The villainous plan in Freedom Force is to provide "The power of ENERGY X" to the most unlawful and nefarious examples of humanity. Mentor rebels and spreads "The power of ENERGY X" to the heroes.

F.E.A.R.'s plot is pretty much entirely centered around one Phlebotinum Rebel escaping after the other - and each one is more willing to kill you in more horrific ways than the last. First off, we have Paxton Fettel, the psychic commander of a cloned army of telepathic-sensitive Super Soldiers. He likes a quick bite to eat and has a bone to pick with Armacham Technology Corporation. But it turns out his real goal is to release Alma, his mother, who is the very angry psychic ghost of a dead girl whose body was used in horrifically cruel experiments. And after Fettel is killed by the Point Man, those very same clone supersoldiers are now working on their own. And they don't like you.

In Warcraft 3, the evil Lich King and his undead scourge rebelled from the also evil Burning Legion as something between a FaustianRebel and a Phlebotinum Rebel. And then a group of semi-evilstruck after Battle for the UndercityChaotic Neutral undead called the forsaken rebelled from HIM.

The Knights of the Ebon Blade in World of Warcraft also arguably fall under this trope. They're undead super soldiers created by the Lich King by re-animating dead Horde and Alliance heroes, whose ostensible purpose was slaughtering the Scarlet Crusade and Argent Dawn. In truth, they were used as the bait in an elaborate Batman Gambit to draw TirionFordring out of hiding. They ended up going rogue at the Battle of Light's Hope Chapel, once their free will was restored and it became apparent that the Lich King betrayed them.

Grey is a textbook Case C; if Mick and Robin weren't snooping around the labs, the Big Bad would still have his backup body. Pandora only added fuel to the flames of rebellion.

This comes up in two games from the Dept. Heaven series. Nessiah was made a Grim Angel against his will, refused to fight, and was thrown out of Asgard blind and wingless with his greatest powers sealed. Cue a thousand-year-long Gambit Roulette that only narrowly fails to take down the entire corrupt system of Asgard. Then Ein comes to the conclusion that sacrificing an entire world and countless angels for the villain to become God isn't cool. Awesomenessensues.

The entire point of Prototype. The government decides to play around with a rather nasty form of viral Phlebotinum, it turns out rather badly for them.

The Kingdom Hearts series has Xion, a living puppet created in the lab as part of their master plan. It...doesn't work out well, as soon as she finds out. To a lesser extent, the Riku Replica does much the same.

Kanden of Metroid Prime: Hunters is a textbook type B example. He was created as a supersoldier for his race, but his mind couldn't handle the stress. The result was he went insane and escaped the facility, destroying it on his way out. After that, he became a bounty hunter, since it would allow him to get paid for the pleasure of hunting down prey.

Juji Kabane in Gungrave: Ovedose was used as a lab rat for gruesome necrolyzation experiments, eventually being transformed into an unstable Deadman/Orgman hybrid. He seeks revenge on the guy who made him this way.

Dragon Age II companion Fenris was branded with lyrium to make an effective body guard for his master. It worked...until he found that he liked being free better than being a slave.

The metaplot of the Assassin's Creed series implies that the ultimate ancestors of the Assassins (and Templars), who are fighting a shadow war for humanity's future, were "Adam and Eve", who were Half Human Hybrids created by The Ones Who Came Before in an effort to pass on some of their powers of knowledge to humans. In their time, however, Adam and Eve apparently used these powers to rebel against the First Civilization; the ensuing conflict was then rendered moot by The End of the World as We Know It.

Paradigm Shift: The Government created artificial werewolves, who (besides transforming to a furry clawed shape) are extremely strong and extremely aggressive, are difficult to injure and heal supernaturally fast. The unwilling subjects this was first tested on mostly died, but two of them survived and are now at large and not cooperating with the Government.

Schlock Mercenary had Massey Reinstein who was kidnapped by the Partnership Collective (TM) and implanted with a device that let him access the attorney drone Hive Mind's vast legal database, but was rescued before they got around to brainwashing him and fully jacking him into the hivemind. Now, he uses their enormous knowledge of the law for good as... Massey Reinstein. He reasoned the safest place from whoever they may send after him is behind some mercenaries and became the lawyer for Tagon's Toughs. As a bonus, Toughs were named as agents of the UNS Superior Court for purpose of administering punitive damages against Partnership Collective, which would be about a million of drones. Massey normally avoids violence, but takes an opportunity to personally kill them whenever he can.

The Renegades from Elf Blood, particularly TKO and JN, are this. Although TKO is the only one particularly bothered about actively destroying the Council, their experimentors.

Terrence of Kate Modern was captured by Michelle Clore and brainwashed into being a psychotic maniac. He was also physically augmented with "Shadow drugs" and given elite combat training. Unfortunately, the training did not include teaching him to know when to shut up. Attempting to forcibly silence him probably wasn't a smart move, either...

Captain Scarlet, in both marionette and CG versions, was empowered by the enemy as an indestructible clone of the original, but overcame his brainwashing. Unusually for this trope, the enemy can still produce unlimited quantities of soldiers with identical powers.

The episode "Alpha" of the 1990 The Flash series had essentially the same plot, except in that case the killer-android-turned-pacifist was a statuesque woman. So The Zeta Project was essentially a spinoff based on a knockoff.

The titular Humongous Mecha of Megas XLR originally was a Gloft Prototype, before stolen and modified by the human resistance, and then modified even further by Coop.

The obscure cartoon Project G.e.e.K.e.R. revolved around this. Female lead steals something important from an evil corporation. It turns out to be the titular Geeker... who was going to be a nearly-omnipotent brainwashed supersoldier, but was taken before his conditioning, and thus has the mind of a child and no real control over his powers. As is usual for this trope. Note to Mad Scientists everywhere—if you're going to give destructive powers to someone, do the brainwashing first!

South Park parodied this with Towelie, a super-towel who becomes sentient and could towel you... to death! If he wasn't busy getting high, that is.

In Code Lyoko, Franz Hopper rebelled against "Project Carthage" which he helped to create, programming XANA to destroy said project. And then XANA rebelled against him.

Occurs a couple of times in Teenage Mutant Ninja Turtles (2003). During the first season, it is shown that the Foot had once mutated several humans in order to enable them to dig deep underground. Eventually, the mutants rebel, killing everyone in their lab and escaping. Later, in the third season, it is revealed that ancient Y'Lyntians had mutated humans and turned them to slaves, before these rebelled and destroyed almost the entire civilization.

The Argentinian android superhero Cybersix rebelled against the evil scientist who created her.

As does her brother Data 7, when he gets his memory back.

Used in Street Sharks, with humans mutated into fish people keeping their original personalities. Unfortunately, Doctor Paradigm didn't realize this when he used the sons of a man he just mutated and forced into hiding has his first test subjects. And he apparently doesn't learn for awhile, since he later uses one of his students as another subject. Neither case turns out too well.

Well he TRIED to add some obediance/mind-control-serum into the mutatgen cocktail starting with his student, but it just wasnt up to snuff and he lost control.